QC Report

	general
Report generated at	2021-03-27 10:03:17
Title	e2f4_mmcf7
Description	chipseq of e2f4_mmcf7
Pipeline version	v1.3.6
Pipeline type	tf
Genome	hg38
Aligner	bowtie2
Sequencing endedness	{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}, 'rep3': {'paired_end': False}, 'rep4': {'paired_end': False}, 'ctl1': {'paired_end': False}, 'ctl2': {'paired_end': False}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	rep3	rep4	ctl1	ctl2
Total Reads	13574853	23241747	21693319	18277255	27421049	21376648
Total Reads (QC-failed)	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0
Mapped Reads	12359177	21082104	10377358	8922391	27031764	21047898
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	91.0	90.7	47.8	48.8	98.6	98.5
Paired Reads	0	0	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	0	0	0	0	0	0
Read1 (QC-failed)	0	0	0	0	0	0
Read2	0	0	0	0	0	0
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	0	0	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0	0.0	0.0
With itself	0	0	0	0	0	0
With itself (QC-failed)	0	0	0	0	0	0
Singletons	0	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	rep3	rep4	ctl1	ctl2
Unpaired Reads	10549101	17962986	8766397	7547567	23134990	18037179
Paired Reads	0	0	0	0	0	0
Unmapped Reads	0	0	0	0	0	0
Unpaired Duplicate Reads	185335	438161	635028	473614	264808	179024
Paired Duplicate Reads	0	0	0	0	0	0
Paired Optical Duplicate Reads	0	0	0	0	0	0
% Duplicate Reads	1.7569000000000001	2.4392	7.2439	6.2751	1.1446	0.9924999999999999

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8, for paired-end)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

SAMstat (filtered/deduped BAM)

	rep1	rep2	rep3	rep4	ctl1	ctl2
Total Reads	10549101	17962986	8766397	7547567	23134990	18037179
Total Reads (QC-failed)	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0
Mapped Reads	10549101	17962986	8766397	7547567	23134990	18037179
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0	100.0	100.0
Paired Reads	0	0	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	0	0	0	0	0	0
Read1 (QC-failed)	0	0	0	0	0	0
Read2	0	0	0	0	0	0
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	0	0	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0	0.0	0.0
With itself	0	0	0	0	0	0
With itself (QC-failed)	0	0	0	0	0	0
Singletons	0	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	0	0	0

Filtered and duplicates removed

Sequence quality metrics (filtered/deduped BAM)

Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.

Library complexity quality metrics

Library complexity (filtered non-mito BAM)

	rep1	rep2	rep3	rep4	ctl1	ctl2
Total Fragments	10543623	17953761	8761258	7543179	23101372	18010826
Distinct Fragments	10359262	17518148	8128219	7071049	22853063	17842892
Positions with Two Read	175790	408695	559459	424512	229171	155840
NRF = Distinct/Total	0.982514	0.975737	0.927746	0.93741	0.989251	0.990676
PBC1 = OneRead/Distinct	0.982669	0.976013	0.926793	0.9367	0.989687	0.991034
PBC2 = OneRead/TwoRead	57.908425	41.835447	13.465108	15.602501	98.692186	113.468326

Mitochondrial reads are filtered out by default. The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads in a dataset; it is the ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair. PBC1 is the primary measure, and the PBC1 should be close to 1. Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs. The PBC2 should be significantly greater than 1. See more details at the ENCODE portal standard for ChIP-Seq pipeline

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Replication quality metrics

IDR (Irreproducible Discovery Rate) plots

Reproducibility QC and peak detection statistics

	overlap	idr
Nt	1400	423
N1	584	339
N2	956	434
N3	6811	99
N4	4646	76
Np	1174	569
N optimal	1400	569
N conservative	1400	423
Optimal Set	rep3_vs_rep4	pooled-pr1_vs_pooled-pr2
Conservative Set	rep3_vs_rep4	rep1_vs_rep2
Rescue Ratio	1.192504258943782	1.3451536643026005
Self Consistency Ratio	11.662671232876713	5.7105263157894735
Reproducibility Test	borderline	borderline

Reproducibility QC

N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Ni: Replicate i self-consistent peaks (comparing two pseudoreplicates generated by subsampling RepX reads)
Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)
Np: Pooled-pseudoreplicate consistent peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2)
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

Number of raw peaks

	rep1	rep2	rep3	rep4
Number of peaks	11861	27393	79034	305432

Top 500000 raw peaks from macs2 with p-val threshold 0.01

Peak calling statistics

Peak region size

	rep1	rep2	rep3	rep4	idr_opt	overlap_opt
Min size	225.0	155.0	140.0	125.0	161.0	161.0
25 percentile	225.0	155.0	140.0	125.0	356.0	161.0
50 percentile (median)	225.0	155.0	140.0	125.0	486.0	227.0
75 percentile	265.0	189.0	140.0	125.0	644.0	418.5
Max size	1155.0	1190.0	885.0	1202.0	1272.0	1272.0
Mean	259.7486721187084	182.76212901106123	151.34878659817295	136.4845693967888	518.5114235500879	323.9971428571429

Enrichment / Signal-to-noise ratio

Strand cross-correlation measures (trimmed/filtered SE BAM)

	rep1	rep2	rep3	rep4
Number of Subsampled Reads	10543623	15000000	8761258	7543179
Estimated Fragment Length	225	155	140	125
Cross-correlation at Estimated Fragment Length	0.132854830863797	0.177195980865676	0.103393071499501	0.0919702009263384
Phantom Peak	50	50	50	50
Cross-correlation at Phantom Peak	0.1346978	0.1788654	0.1052606	0.09369839
Argmin of Cross-correlation	1500	1500	1500	1500
Minimum of Cross-correlation	0.1315826	0.1757141	0.1021858	0.09091598
NSC (Normalized Strand Cross-correlation coeff.)	1.009669	1.008433	1.011815	1.011596
RSC (Relative Strand Cross-correlation coeff.)	0.4084002	0.4702446	0.3926369	0.378888

Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50. Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only. Untrimmed FASTQs are used for all the other analyses.

NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value

Jensen-Shannon distance (filtered/deduped BAM)

	rep1	rep2	rep3	rep4
AUC	0.2348575091536404	0.2656754299983346	0.211893377910859	0.20232067091931763
Synthetic AUC	0.48452963388008585	0.48814411820721243	0.483028504386599	0.48170713791558367
X-intercept	0.264355176660642	0.16215351641848338	0.331602581532605	0.37227291630012316
Synthetic X-intercept	5.847803465011934e-35	4.145764359054296e-60	6.197801217755861e-29	8.061681714050388e-25
Elbow Point	0.5586342988755778	0.5405603717151037	0.623070648262184	0.662733321603941
Synthetic Elbow Point	0.5178502171302848	0.4990978226632539	0.5222627040439207	0.5044200485168939
JS Distance	0.060823917898187835	0.038915704132794375	0.06848516614175386	0.07262149939819024
Synthetic JS Distance	0.2429608847997283	0.25588835296994555	0.24318949406530596	0.23330479427675338
% Genome Enriched	43.11091473264983	44.059196110107	36.7512515794693	32.8165736312599
Diff. Enrichment	24.457534287251566	17.38062031598082	29.45704334622596	31.349798540380604
CHANCE Divergence	0.22848732897527158	0.1596427735755121	0.26550148533444506	0.27673551418763154

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for macs2 raw peaks

	rep1	rep2	rep3	rep4	rep1-pr1	rep2-pr1	rep3-pr1	rep4-pr1	rep1-pr2	rep2-pr2	rep3-pr2	rep4-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.008662254726729794	0.012034302092090925	0.040494971879553254	0.11946088057250767	0.014554035025919742	0.01815321795607924	0.11676038436767301	0.09879261770149007	0.014661345517627097	0.018069044868152768	0.1166232965063408	0.098754220897174	0.005019581135978273	0.009916465098623225	0.009769498305984949

FRiP for overlap peaks

	rep1_vs_rep2	rep1_vs_rep3	rep1_vs_rep4	rep2_vs_rep3	rep2_vs_rep4	rep3_vs_rep4	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	rep4-pr1_vs_rep4-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.0018073418958988825	0.0017263621995165267	0.0017382079898137803	0.0018302749889790649	0.0018993196612389523	0.001952837647911479	0.0018311512990538245	0.001982242818649416	0.0056034423264198505	0.0045665046762751495	0.0020388367469621627

FRiP for IDR peaks

	rep1_vs_rep2	rep1_vs_rep3	rep1_vs_rep4	rep2_vs_rep3	rep2_vs_rep4	rep3_vs_rep4	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	rep4-pr1_vs_rep4-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.0015375657338184887	0.001367686839065971	0.0014212717511074085	0.001448778077729845	0.0015055084821101016	0.0013634259239119681	0.0015384249330819754	0.0016047443337093288	0.0005367085246082285	0.00045431859034838644	0.0016845115354908243

For macs2 raw peaks:

repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)

For overlap/IDR peaks:

repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates